mad-search 0.1.0__tar.gz

mad_search-0.1.0/.gitignore

@@ -0,0 +1,13 @@
+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# Search config files (contain API keys)
+search.md

mad_search-0.1.0/.python-version

@@ -0,0 +1 @@
+3.14

mad_search-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 The mad-search authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mad_search-0.1.0/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.4
+Name: mad-search
+Version: 0.1.0
+Summary: Search OpenAlex for academic articles using YAML-frontmatter markdown files
+Project-URL: Homepage, https://codeberg.org/divinemadman/mad-search
+Project-URL: Repository, https://codeberg.org/divinemadman/mad-search.git
+Project-URL: Issues, https://codeberg.org/divinemadman/mad-search/issues
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: pyalex>=0.21
+Requires-Dist: pyyaml>=6.0
+Description-Content-Type: text/markdown
+
+# mad-search
+
+[![Codeberg](https://img.shields.io/badge/hosted-Codeberg-2185D0?logo=codeberg)](https://codeberg.org/divinemadman/mad-search)
+
+Search OpenAlex for academic articles using YAML-frontmatter markdown files.
+
+## Requirements
+
+- Python 3.13+
+- A free [OpenAlex API key](https://openalex.org/settings/api)
+
+## Installation
+
+```bash
+# run directly with uv
+uv run mad-search path/to/search.md
+
+# or install globally
+uv tool install mad-search
+```
+
+## Usage
+
+Create a markdown file with YAML frontmatter:
+
+```markdown
+---
+api_key: your_key_here
+query: "(machine learning AND climate) OR large language models"
+journals:
+  - Nature
+  - Science
+year_from: 2020
+year_to: 2025
+---
+```
+
+Run it:
+
+```bash
+uv run mad-search search.md
+```
+
+Results are appended to the same file, overwriting any previous results.
+
+## Features
+
+- **Boolean search** — `AND`, `OR`, `NOT` with parentheses, passed directly to OpenAlex's Elasticsearch backend
+- **Journal filter** — names auto-resolved to ISSNs via the OpenAlex Sources endpoint
+- **Year range** — optional `year_from` / `year_to` constraints
+- **Result re-ranking** — results scored by title match (40%), abstract match (20%), and concept overlap (40%) after retrieval
+- **Structured output** — summary table plus detail sections with DOI, citation count, FWCI, concepts (top 5, score ≥ 0.3), and abstract
+- **Idempotent** — re-running replaces the previous results section
+
+## Output
+
+Results are appended as a markdown table with detail sections:
+
+```markdown
+## Results — 5 paper(s) found
+
+| # | Title | DOI | Journal | Year | Citations | Authors |
+|---|---|---|---|---|---|---|
+
+---
+
+### 1. Paper Title
+
+- **DOI:** `10.xxx/...`
+- **Authors:** ...
+- **Journal:** ...
+- **Citations:** 124 | FWCI: 3.2
+- **Concepts:** Climate Science (0.92), Machine Learning (0.87)
+- **Abstract:** ...
+```
+
+## License
+
+MIT — see [LICENSE](LICENSE).

mad_search-0.1.0/README.md

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+# mad-search
+
+[![Codeberg](https://img.shields.io/badge/hosted-Codeberg-2185D0?logo=codeberg)](https://codeberg.org/divinemadman/mad-search)
+
+Search OpenAlex for academic articles using YAML-frontmatter markdown files.
+
+## Requirements
+
+- Python 3.13+
+- A free [OpenAlex API key](https://openalex.org/settings/api)
+
+## Installation
+
+```bash
+# run directly with uv
+uv run mad-search path/to/search.md
+
+# or install globally
+uv tool install mad-search
+```
+
+## Usage
+
+Create a markdown file with YAML frontmatter:
+
+```markdown
+---
+api_key: your_key_here
+query: "(machine learning AND climate) OR large language models"
+journals:
+  - Nature
+  - Science
+year_from: 2020
+year_to: 2025
+---
+```
+
+Run it:
+
+```bash
+uv run mad-search search.md
+```
+
+Results are appended to the same file, overwriting any previous results.
+
+## Features
+
+- **Boolean search** — `AND`, `OR`, `NOT` with parentheses, passed directly to OpenAlex's Elasticsearch backend
+- **Journal filter** — names auto-resolved to ISSNs via the OpenAlex Sources endpoint
+- **Year range** — optional `year_from` / `year_to` constraints
+- **Result re-ranking** — results scored by title match (40%), abstract match (20%), and concept overlap (40%) after retrieval
+- **Structured output** — summary table plus detail sections with DOI, citation count, FWCI, concepts (top 5, score ≥ 0.3), and abstract
+- **Idempotent** — re-running replaces the previous results section
+
+## Output
+
+Results are appended as a markdown table with detail sections:
+
+```markdown
+## Results — 5 paper(s) found
+
+| # | Title | DOI | Journal | Year | Citations | Authors |
+|---|---|---|---|---|---|---|
+
+---
+
+### 1. Paper Title
+
+- **DOI:** `10.xxx/...`
+- **Authors:** ...
+- **Journal:** ...
+- **Citations:** 124 | FWCI: 3.2
+- **Concepts:** Climate Science (0.92), Machine Learning (0.87)
+- **Abstract:** ...
+```
+
+## License
+
+MIT — see [LICENSE](LICENSE).

mad_search-0.1.0/pyproject.toml

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+[project]
+name = "mad-search"
+version = "0.1.0"
+description = "Search OpenAlex for academic articles using YAML-frontmatter markdown files"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "pyalex>=0.21",
+    "pyyaml>=6.0",
+]
+
+[project.urls]
+Homepage = "https://codeberg.org/divinemadman/mad-search"
+Repository = "https://codeberg.org/divinemadman/mad-search.git"
+Issues = "https://codeberg.org/divinemadman/mad-search/issues"
+
+[project.scripts]
+mad-search = "mad_search.__main__:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/mad_search"]

mad_search-0.1.0/src/mad_search/__init__.py

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+from .models import SearchConfig, WorkResult
+from .search import run_search
+from .config import parse_frontmatter
+
+__all__ = ["SearchConfig", "WorkResult", "run_search", "parse_frontmatter"]

mad_search-0.1.0/src/mad_search/__main__.py

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+import sys
+from pathlib import Path
+
+import pyalex
+
+from .config import parse_frontmatter
+from .journals import resolve_journals
+from .search import run_search
+from .formatter import format_results
+
+
+def main() -> None:
+    if len(sys.argv) != 2:
+        print("Usage: mad-search <path/to/search.md>")
+        sys.exit(1)
+
+    filepath = Path(sys.argv[1])
+    if not filepath.exists():
+        print(f"Error: file not found: {filepath}")
+        sys.exit(1)
+
+    try:
+        config, body = parse_frontmatter(filepath)
+    except ValueError as e:
+        print(f"Error: {e}")
+        sys.exit(1)
+
+    pyalex.config.api_key = config.api_key
+
+    print(f"Query: {config.query}")
+    if config.journals:
+        print(f"Journals: {', '.join(config.journals)}")
+    if config.year_from or config.year_to:
+        print(f"Year range: {config.year_from or 'any'} \u2014 {config.year_to or 'any'}")
+
+    issns = resolve_journals(config.journals)
+    if config.journals and not issns:
+        print("Error: none of the specified journals could be resolved.")
+        sys.exit(1)
+    if issns:
+        print(f"Resolved ISSNs: {', '.join(issns)}")
+
+    print("Searching OpenAlex\u2026")
+
+    try:
+        results = run_search(config, issns)
+    except RuntimeError as e:
+        print(f"Error: {e}")
+        sys.exit(1)
+
+    print(f"Found {len(results)} result(s)")
+
+    output = format_results(results)
+
+    content = filepath.read_text(encoding="utf-8")
+
+    if "## Results" in content:
+        content = content[: content.index("## Results")].rstrip()
+
+    filepath.write_text(content + "\n\n" + output + "\n", encoding="utf-8")
+    print(f"Written to {filepath}")
+
+
+if __name__ == "__main__":
+    main()

mad_search-0.1.0/src/mad_search/config.py

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+import re
+from pathlib import Path
+
+import yaml
+
+from .models import SearchConfig
+
+
+def parse_frontmatter(path: Path) -> tuple[SearchConfig, str]:
+    content = path.read_text(encoding="utf-8")
+
+    match = re.match(r"^---\s*\n(.*?)\n\s*---\s*\n?(.*)", content, re.DOTALL)
+    if not match:
+        raise ValueError(
+            "No YAML frontmatter found. "
+            "File must start with `---\\n...\\n---`."
+        )
+
+    raw_yaml = match.group(1)
+    body = match.group(2)
+
+    try:
+        data = yaml.safe_load(raw_yaml)
+    except yaml.YAMLError as e:
+        raise ValueError(f"Invalid YAML frontmatter: {e}")
+
+    if not isinstance(data, dict):
+        raise ValueError("YAML frontmatter must be a mapping (key: value pairs)")
+
+    api_key = data.get("api_key")
+    if not api_key:
+        raise ValueError(
+            "`api_key` is required in frontmatter. "
+            "Get one at https://openalex.org/settings/api"
+        )
+
+    query = data.get("query")
+    if not query:
+        raise ValueError("`query` is required in frontmatter")
+
+    config = SearchConfig(
+        api_key=str(api_key),
+        query=str(query),
+        journals=data.get("journals", []) or [],
+        year_from=data.get("year_from"),
+        year_to=data.get("year_to"),
+    )
+
+    return config, body

mad_search-0.1.0/src/mad_search/formatter.py

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+from .models import WorkResult
+
+
+def format_results(results: list[WorkResult]) -> str:
+    lines: list[str] = []
+
+    if not results:
+        lines.append("## Results")
+        lines.append("")
+        lines.append("*No results found.*")
+        return "\n".join(lines)
+
+    lines.append(f"## Results \u2014 {len(results)} paper(s) found")
+    lines.append("")
+
+    lines.append("| # | Title | DOI | Journal | Year | Citations | Authors |")
+    lines.append("|---|---|---|---|---|---|---|")
+    for i, r in enumerate(results, start=1):
+        authors_str = ", ".join(r.authors[:3])
+        if len(r.authors) > 3:
+            authors_str += " et al."
+        title = (r.title or "N/A")[:80]
+        doi = r.doi or "N/A"
+        journal = (r.journal or "N/A")[:40]
+        year = str(r.year or "N/A")
+        citations = f"{r.cited_by_count:,}" if r.cited_by_count is not None else "N/A"
+        lines.append(f"| {i} | {title} | {doi} | {journal} | {year} | {citations} | {authors_str} |")
+
+    lines.append("")
+    lines.append("---")
+    lines.append("")
+
+    for i, r in enumerate(results, start=1):
+        lines.append(f"### {i}. {r.title or 'Untitled'}")
+        lines.append("")
+        lines.append(f"- **DOI:** `{r.doi or 'N/A'}`")
+        lines.append(f"- **Authors:** {', '.join(r.authors) or 'N/A'}")
+        lines.append(f"- **Journal:** {r.journal or 'N/A'} ({r.year or 'N/A'})")
+        if r.openalex_id:
+            lines.append(f"- **OpenAlex:** [{r.openalex_id}]({r.openalex_id})")
+        if r.cited_by_count is not None:
+            fwci_str = f" | FWCI: {r.fwci:.1f}" if r.fwci is not None else ""
+            lines.append(f"- **Citations:** {r.cited_by_count:,}{fwci_str}")
+        if r.concepts:
+            concepts_str = ", ".join(f"{c['name']} ({c['score']:.2f})" for c in r.concepts)
+            lines.append(f"- **Concepts:** {concepts_str}")
+        if r.abstract:
+            abstract = r.abstract[:1000]
+            suffix = "\u2026" if len(r.abstract) > 1000 else ""
+            lines.append(f"- **Abstract:** {abstract}{suffix}")
+        lines.append("")
+
+    return "\n".join(lines)

mad_search-0.1.0/src/mad_search/journals.py

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+from pyalex import Sources
+
+
+def resolve_journals(names: list[str]) -> list[str]:
+    if not names:
+        return []
+
+    resolved: list[str] = []
+
+    for name in names:
+        try:
+            results = list(Sources().search(name).filter(type="journal").get(per_page=3))
+        except Exception as e:
+            print(f"  \u26a0 Error looking up journal '{name}': {e}")
+            continue
+
+        if not results:
+            print(f"  \u26a0 Could not resolve journal: '{name}'")
+            continue
+
+        source = results[0]
+        issn = source.get("issn_l") or (source.get("issn") or [None])[0]
+        if issn:
+            resolved.append(issn)
+            print(f"  \u2713 {name} \u2192 {issn}")
+        else:
+            print(f"  \u26a0 Journal '{name}' found but has no ISSN")
+
+    return resolved

mad_search-0.1.0/src/mad_search/models.py

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+from dataclasses import dataclass, field
+from typing import Optional
+
+
+@dataclass
+class SearchConfig:
+    api_key: str
+    query: str
+    journals: list[str] = field(default_factory=list)
+    year_from: Optional[int] = None
+    year_to: Optional[int] = None
+
+
+@dataclass
+class WorkResult:
+    doi: Optional[str]
+    title: Optional[str]
+    authors: list[str]
+    journal: Optional[str]
+    year: Optional[int]
+    openalex_id: Optional[str]
+    abstract: Optional[str]
+    concepts: list[dict] = field(default_factory=list)
+    cited_by_count: Optional[int] = None
+    fwci: Optional[float] = None

mad_search-0.1.0/src/mad_search/rerank.py

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+import re
+
+from .models import WorkResult
+
+STOP_WORDS = {"the", "a", "an", "of", "in", "on", "at", "to", "for", "and", "or", "not", "is", "by", "with",
+              "from", "as", "be", "this", "that", "it", "its"}
+
+
+def _extract_terms(query: str) -> list[str]:
+    cleaned = re.sub(r"\b(?:AND|OR|NOT)\b", " ", query)
+    cleaned = re.sub(r"[()\"'']", " ", cleaned)
+    tokens = [t.lower() for t in cleaned.split()
+              if t.lower() not in STOP_WORDS and len(t) > 1]
+    return list(set(tokens))
+
+
+def _title_score(title: str | None, terms: list[str]) -> float:
+    if not title or not terms:
+        return 0.0
+    t = title.lower()
+    return sum(1 for term in terms if term in t) / len(terms)
+
+
+def _abstract_score(abstract: str | None, terms: list[str]) -> float:
+    if not abstract or not terms:
+        return 0.0
+    a = abstract.lower()
+    return sum(1 for term in terms if term in a) / len(terms)
+
+
+def _concept_score(concepts: list[dict], terms: list[str]) -> float:
+    if not concepts or not terms:
+        return 0.0
+    total = 0.0
+    count = 0
+    for c in concepts:
+        name = c["name"].lower()
+        if any(term in name or name in term for term in terms):
+            total += c["score"]
+            count += 1
+    return total / count if count else 0.0
+
+
+def rerank(results: list[WorkResult], query: str) -> list[WorkResult]:
+    terms = _extract_terms(query)
+    if not terms:
+        return results
+
+    scored: list[tuple[float, WorkResult]] = []
+    for r in results:
+        ts = _title_score(r.title, terms)
+        aps = _abstract_score(r.abstract, terms)
+        cs = _concept_score(r.concepts, terms)
+        combined = 0.4 * ts + 0.2 * aps + 0.4 * cs
+        scored.append((combined, r))
+
+    scored.sort(key=lambda x: x[0], reverse=True)
+    return [r for _, r in scored]

mad_search-0.1.0/src/mad_search/search.py

@@ -0,0 +1,131 @@
+import re
+
+from pyalex import Works
+
+from .models import SearchConfig, WorkResult
+from .rerank import rerank
+
+
+def decode_abstract(inverted_index: dict | None) -> str | None:
+    if not inverted_index:
+        return None
+    max_pos = max(max(positions) for positions in inverted_index.values())
+    words = [""] * (max_pos + 1)
+    for word, positions in inverted_index.items():
+        for pos in positions:
+            words[pos] = word
+    return " ".join(words)
+
+
+def _split_or_query(query: str) -> list[str]:
+    parts = []
+    depth = 0
+    start = 0
+    i = 0
+    while i < len(query):
+        if query[i] == "(":
+            depth += 1
+        elif query[i] == ")":
+            depth -= 1
+        elif depth == 0 and query[i:i+4] == " OR ":
+            parts.append(query[start:i].strip())
+            start = i + 4
+            i += 3
+        i += 1
+    parts.append(query[start:].strip())
+    return [p for p in parts if p]
+
+
+def _strip_operators(s: str) -> str:
+    cleaned = re.sub(r"\b(?:AND|OR|NOT)\b", " ", s)
+    cleaned = re.sub(r"[()\"']", " ", cleaned)
+    return cleaned.strip()
+
+
+def _parse_work(w: dict) -> WorkResult:
+    authors = [
+        a["author"]["display_name"]
+        for a in w.get("authorships", [])
+        if a.get("author")
+    ]
+    primary = w.get("primary_location") or {}
+    source = primary.get("source") or {}
+    journal = source.get("display_name")
+    abstract = decode_abstract(w.get("abstract_inverted_index"))
+    concepts_raw = w.get("concepts", [])
+    concepts = [
+        {"name": c["display_name"], "score": c["score"]}
+        for c in concepts_raw
+        if c.get("score", 0) >= 0.3
+    ][:5]
+    return WorkResult(
+        doi=w.get("doi"),
+        title=w.get("title"),
+        authors=authors,
+        journal=journal,
+        year=w.get("publication_year"),
+        openalex_id=w.get("id"),
+        abstract=abstract,
+        concepts=concepts,
+        cited_by_count=w.get("cited_by_count"),
+        fwci=w.get("fwci"),
+    )
+
+
+def _search_branch(
+    search_q: str,
+    filters: dict,
+    seen_dois: set[str],
+) -> list[WorkResult]:
+    works = (
+        Works()
+        .search(search_q)
+        .filter(**filters)
+        .select([
+            "id", "doi", "title", "authorships",
+            "primary_location", "publication_year",
+            "abstract_inverted_index",
+            "concepts", "cited_by_count", "fwci",
+        ])
+    )
+
+    results: list[WorkResult] = []
+    for page in works.paginate(per_page=200, n_max=1000):
+        for w in page:
+            doi = w.get("doi")
+            if doi:
+                if doi in seen_dois:
+                    continue
+                seen_dois.add(doi)
+            results.append(_parse_work(w))
+    return results
+
+
+def run_search(config: SearchConfig, issns: list[str]) -> list[WorkResult]:
+    filters: dict = {}
+
+    if config.year_from is not None:
+        filters["from_publication_date"] = f"{config.year_from}-01-01"
+    if config.year_to is not None:
+        filters["to_publication_date"] = f"{config.year_to}-12-31"
+    if issns:
+        filters["primary_location"] = {"source": {"issn": "|".join(issns)}}
+
+    branches = _split_or_query(config.query)
+    if not branches:
+        branches = [config.query]
+
+    all_results: list[WorkResult] = []
+    seen_dois: set[str] = set()
+
+    try:
+        for branch in branches:
+            search_q = _strip_operators(branch)
+            if not search_q:
+                continue
+            all_results.extend(_search_branch(search_q, filters, seen_dois))
+    except Exception as e:
+        raise RuntimeError(f"OpenAlex API error: {e}")
+
+    all_results = rerank(all_results, config.query)
+    return all_results

mad_search-0.1.0/uv.lock

@@ -0,0 +1,166 @@
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+
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+version = "2026.6.17"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/c9/c7/424b75da314c1045981bd9777432fad05a9e0c69daa4ed7e308bbaffe405/certifi-2026.6.17.tar.gz", hash = "sha256:024c88eeec92ca068db80f02b8b07c9cef7b9fe261d1d535abfd5abd6f6af432", size = 134594, upload-time = "2026-06-17T10:31:07.894Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ef/2f/c5464532e965badff2f4c4c1a3a83f5697f0d7c407ed0cda44aaa99bb451/certifi-2026.6.17-py3-none-any.whl", hash = "sha256:2227dcbaafe0d2f59279d1762ddddc37783ed4354594f194ffc31d20f41fc3db", size = 133289, upload-time = "2026-06-17T10:31:06.348Z" },
+]
+
+[[package]]
+name = "charset-normalizer"
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